Hi Eric,
First of all the real-time tutorial is a good place to start with real-time applications:
It does not sound like you are doing event response or closed loop control system, so I do not think that real-time operating systems will get you to the goal. Typically if there is no control in your system RT is not needed. You say that the user will change gain, attenuation, polarity, etc but is deterministic control really needed (speed is not equivalent to real-time).
A few questions may flesh out the best solution.
1) Is the black box taking care of all the data collection?
2) Is determinism required in any part of the project?
3) Are you trying to do control over ethernet? This is hard because ethernet is effected by many different variables, and is not deterministic.
4) Where is the user interfacing to change the gain, attenuation, polarity, etc ?
I definitly think that NI products can give you a solution, what is really needed will give you the best solution.
Brian K.